A spectrum analyzer can be used to measure jitter of a CW signal at some carrier frequency. This is done by putting the signal directly into the input of the analyzer and making a measurement in the frequency domain of the spectrum surrounding the CW signal. This is called the single sideband phase noise. To get the jitter, we use a marker in the spectrum analyzer and integrate over the single sideband phase noise spectrum. The analyzer performs all the required corrections and calculations and gives the final answer in terms of overall jitter. There is a great article that summarizes these measurements located here: http://mwrf.com/test-amp-measurement-analyzers/demystify-integrated-phase-deviation-results-phase-noise-measurements

Normally, for the contribution to overall jitter from a PLL, you would be measuring the jitter from the reference clock (amplified by a multiplier or reduced with a divider) combined with the jitter contribution from the VCO (voltage controlled oscillator). In general, thorough analysis of a clock signal requires femto second accuracy which can really only be achieved using a phase noise measurement technique. The signal analyzer measurement technique is known as a direct spectrum method. It is useful because it is the easiest method, but there are tradeoffs associated with it. The analyzer can perform some AM rejection, but it is not perfect, so separating the noise types can be difficult. Also, the analyzer's dynamic range can be an issue for high performance PLL's. You can determine whether this is true by looking at the phase noise specification in the data sheet or specs guide for the given signal analyzer. In the case where the signal analyzer does not have enough dynamic range, then other phase noise measurement techniques should be considered. Here is a link to a phase noise measurement selection guide which should help you determine which solution is best for your needs: http://cp.literature.agilent.com/litweb/pdf/5990-5729EN.pdf

Also, I will give you a link to this application note about measuring clock jitter using phase noise measurement techniques: http://cp.literature.agilent.com/litweb/pdf/5989-9849EN.pdf

This app note is perfect to help you determine the benefits of this technique and whether it would satisfy your need.

Please let me know if you have any additional questions. Best Regards, Scott